Numerous studies have shown decreased function of the adrenal (stress handler) gland in CFS. This is one more study showing that morning cortisol levels are significantly lower in CFS—but only in women. Cortisol levels should be highest in the morning, giving you a "jump start" to begin your day. Most studies have not shown the low cortisol problem to only occur in women, but it will be interesting to watch as more research comes out.
For a review article on adrenal issues in CFS/FMS, see The Adrenal Gland.
Attenuated Morning Salivary Cortisol Concentrations in a Population-based Study of Persons with Chronic Fatigue Syndrome and Well Controls
Journal: J Clin Endocrinol Metab. 2007 Dec 26 [Epub ahead of print]
Authors: Nater UM [1,2], Maloney E , Boneva RS , Gurbaxani BM [1,3], Lin JM , Jones JF , Reeves WC, Heim C. 
Affiliations:  Chronic Viral Diseases Branch, Coordinating Center for Infectious Diseases, Centers for Disease Control & Prevention, Atlanta, GA;  Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA;  Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA.
NLM Citation: PMID: 18160468
Context: A substantial body of research on the pathophysiology of chronic fatigue syndrome (CFS) has focused on hypothalamic-pituitary-adrenal (HPA) axis dysregulation. The cortisol awakening response has received particular attention as a marker of HPA axis dysregulation.
Objective: The objective of the current study was to evaluate morning salivary cortisol profiles in persons with CFS and well controls identified from the general population.
Design: Case-control study.
Setting: This study was conducted at an outpatient research clinic.
Cases and Other Participants: We screened a sample of 19,381 residents of Georgia and identified those with CFS and a matched sample of well controls. Seventy-five medication-free CFS cases and 110 medication-free well controls provided complete sets of saliva samples.
Main Outcome Measures: Free cortisol concentrations in saliva collected on a regular workday, immediately upon awakening, 30 minutes and 60 minutes after awakening.
Results: There was a significant interaction effect, indicating different profiles of cortisol concentrations over time between groups, with the CFS group showing an attenuated morning cortisol profile. Notably, we observed a sex difference in this effect. Women with CFS exhibited significantly attenuated morning cortisol profiles compared with well women. In contrast, cortisol profiles were similar in men with CFS and male controls.
Conclusions: CFS was associated with an attenuated morning cortisol response but the effect was limited to women. Our results suggest that a sex difference in hypocortisolism may contribute to increased risk of CFS in women.
[Note: The full text is currently available for free in PDF format at http://jcem.endojournals.org/cgi/rapidpdf/jc.2007-1747v1]